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Intelligent Design proponents are fond of saying that Darwin considered the cell to be just a formless blob of protoplasm. Behe’s Darwin’s Black Box is a good example of this kind of silliness. Few IDiots realize that Darwin was, in fact, a first rate microscopist. In this experiment we see Darwin at the microscope. We also see that he was aware that cells were more than just vague bits of protoplasm.

In my ‘Insectivorous Plants’ I have described, under the term of aggregation, a phenomenon which has excited the surprise of all who have beheld it*. It is best exhibited in the tentacles or so-called glandular hairs of Drosera, when a minute particle of any solid substance, or a drop of almost any nitrogenous fluid, is placed on a gland. Under favourable circumstances the transparent purple fluid in the cells nearest to the gland becomes in a few seconds or minutes slightly turbid. Soon minute granules can be distinguished under a high power, which quickly coalesce or grow larger; and for many hours afterwards oval or globular, or curiously-shaped masses of a purple colour and of considerable size may be observed sending out processes or filaments, dividing, coalescing, and redividing in the most singular manner, until finally one or two solid spheres are formed which remain motionless. The moving masses include vacuoles which change their appearance. (I append here three figures of aggregated masses copied from my son Francis’s paper†, showing the forms assumed.) After aggregation has been partially effected, the layer of protoplasm lining the walls of the cells may be seen with singular clearness flowing in great waves; and my son observed similarly flowing threads of protoplasm which connected together the grains of chlorophyll. After a time the minute colourless particles which are imbedded in the flowing protoplasm are drawn towards and unite with the aggregated masses; so that the protoplasm on the walls being now rendered quite transparent is no longer visible, though some is still present, and still flows, as may be inferred from the occasional transport of particles in the cell-sap. The granules withdrawn from the walls, together probably with some matter derived from the flowing protoplasm and from the cell-sap, often form a colourless, or very pale purple, well-defined layer of considerable thickness, which surrounds the previously aggregated and now generally spherical dark-purple masses. The surrounding layers or zones consist of solid matter, more brittle than the central parts of the aggregated masses, as could be seen when they were crushed beneath a cover-glass.

Here is a picture:

Darwin goes on to test a wide variety of plants, of which, this one stands out:

Pelargonium zonale.–The effects produced by the immersion of the leaves of this plant for 24 or 48 hours in solutions of 4 or 7 parts of carbonate of ammonia to 1000 of water are not a little perplexing. The leaves are clothed with glandular hairs, which absorb the ammonia and undergo aggregation. Moreover, numerous almost colourless, shining, translucent spheres generally, but not invariably, appear in most of the epidermal cells in which there are no grains of chlorophyll, and in the palisade-cells, in which they abound, and likewise in the parenchyma. The smaller spheres blend together, and thus form large ones. A solution of only 2 to 1000 sometimes sufficed to produce the spheres. Usually the spheres are not acted on by alcohol, but occasionally they were dissolved by it. If after immersion in alcohol they are subjected to the iodine solution, they soon almost disappear; but this, again, does not invariably occur. Acetic acid always caused their rapid disappearance, and without any apparent effervescence, a slight granular residue being sometimes left; and this occurred with leaves which had been kept so long in the solution that they were dead. The acid dissolved, of course with effervescence, the crystalline balls of carbonate of lime which occupy many of the palisade-cells. When sulphuric ether was added, the smaller spheres of transparent matter disappeared in the course of a few minutes, while the larger ones became brownish and granular in their centres; but this granular matter disappeared after a time, empty transparent bag-like membranes being left. Traces of similar membranous envelopes could sometimes be detected after the administration of acetic acid. Caustic potash did not act quickly on the spheres, but sometimes caused them to swell up. I do not know what ought to be inferred from the action of these several reagents with respect to the nature of the spheres and aggregated masses in which I never saw any movement.
On two or three occasions the palisade-cells of leaves which had been immersed in the solutions, instead of containing large transparent spheres, were gorged with innumerable, often irregularly-shaped, more or less confluent globules, many of them being much smaller than the chlorophyll-grains. This occurred with a leaf which had been immersed for only 18½ hours in a solution of 4 to 1000. After sections of this leaf had been cleared with alcohol, it was irrigated with the solution of iodine, and the globules rapidly ran together or became confluent, forming irregular amorphous masses.

Clearly, Darwin was aware that there was more to the cell than protoplasmic goo. Over and above that, this paper is an excellent example of Darwin the experimenter. We see multiple tests on a wide variety of plants, we see different variables being examined and after the results are in we see Darwin relating them back to his original hypothesis.
Update: Wesley R. Elsberry tackles the subject as well – the Johnny-come-lately!

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“Intelligent Design proponents are fond of saying that Darwin considered the cell to be just a formless blob of protoplasm.”
Darwin saw cells as complex thing during his last years. But what he thought about cells, when he wrote the Origins?
There is many decades between writing time of Origins and year 1882. The term protoplasm was coined in 1846. The golden time period of the protoplasm thinking was before the late 1900’s. Many scientist began see the cells as more complex thing in the late 1900’s. Citing what Darwin wrote in 1982 does not counter the claim, that Darwin had considered the cell to be just a formless blob of protoplasm, during the time he was writing the book Origins.
What is the earliest reference, where Darwin does not support the protoplasmic thinking? Was it published in 1882?

…And the goalposts just got moved. ID proponets do not make the narrow claim that Darwin knew nothing about the cell at the time he wrote Origins. They say he knew nothing about it period. However, there are a number of letters written to Lubbock in the 1850’s that make it clear he knew there was more to the cell than protoplasm. There are also some mentions in his transmutation notebooks that appear so indicates the same – although I haven’t had time to completely read the latter yet…

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"You may not be willing to admit that you resemble an ape; if your thousandth ancestor is more like an ape than you are, you may, if you wish, call it a coincidence. But if that thousandth ancestor's forebears become progressively more simian as you trace back the geneological lines, you will have to admit that somewhere in your family tree there squats an ape." Earnest Hooten

Charles Darwin

"But I had gradually come, by this time, to see that the Old Testament from its manifestly false history of the world, with the Tower of Babel, the rainbow at sign, etc., etc., and from its attributing to God the feelings of a revengeful tyrant, was no more to be trusted than the sacred books of the Hindoos, or the beliefs of any barbarian." Charles Darwin: The Autobiography